Starting phenix.real_space_refine (version: dev) on Sun Feb 26 15:30:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2023/8bd5_15975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2023/8bd5_15975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2023/8bd5_15975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2023/8bd5_15975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2023/8bd5_15975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2023/8bd5_15975_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28398 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4899 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Chain: "B" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 5235 Classifications: {'RNA': 246} Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 106, 'rna3p_pyr': 102} Link IDs: {'rna2p': 38, 'rna3p': 207} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 827 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "D" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 840 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2046 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1284 Classifications: {'peptide': 161} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 148} Chain: "X" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 685 Classifications: {'peptide': 85} Link IDs: {'TRANS': 84} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27217 SG CYS Q 133 72.612 119.769 107.506 1.00 71.20 S ATOM 27238 SG CYS Q 136 75.671 117.734 106.864 1.00 77.14 S ATOM 27354 SG CYS Q 151 72.278 116.157 107.379 1.00 78.37 S ATOM 27381 SG CYS Q 154 73.864 117.713 110.203 1.00 81.82 S ATOM 26942 SG CYS Q 100 60.616 127.373 106.385 1.00 74.10 S ATOM 26957 SG CYS Q 103 56.645 126.988 106.822 1.00 77.88 S ATOM 27126 SG CYS Q 122 57.843 129.425 104.971 1.00 82.85 S Time building chain proxies: 15.61, per 1000 atoms: 0.55 Number of scatterers: 28398 At special positions: 0 Unit cell: (136.5, 150.15, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 85 16.00 P 346 15.00 Mg 7 11.99 O 6187 8.00 N 5150 7.00 C 16621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.85 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 154 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 136 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 151 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 133 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 125 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 103 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 100 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 122 " Number of angles added : 9 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 12 sheets defined 55.2% alpha, 5.5% beta 118 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 10.96 Creating SS restraints... Processing helix chain 'A' and resid 14 through 25 removed outlier: 3.791A pdb=" N LEU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 43 through 50 removed outlier: 4.273A pdb=" N GLU A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 67 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 77 through 94 removed outlier: 3.704A pdb=" N SER A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.547A pdb=" N ASN A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.691A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 319 through 338 removed outlier: 4.468A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 384 through 407 removed outlier: 3.583A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 4.201A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'A' and resid 485 through 506 removed outlier: 3.813A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 537 Processing helix chain 'A' and resid 551 through 566 removed outlier: 3.639A pdb=" N VAL A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 619 through 634 Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 136 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 164 removed outlier: 3.883A pdb=" N ALA E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 184 through 189 removed outlier: 4.360A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 removed outlier: 3.691A pdb=" N GLU E 212 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET E 214 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 241 through 258 Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 151 through 164 Processing helix chain 'F' and resid 174 through 182 removed outlier: 3.852A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 203 through 213 removed outlier: 4.260A pdb=" N GLU F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 3.815A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.511A pdb=" N ARG G 74 " --> pdb=" O CYS G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 136 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 164 removed outlier: 3.766A pdb=" N ALA G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 3.551A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 202 through 213 Processing helix chain 'G' and resid 227 through 236 removed outlier: 4.110A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 233 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA G 236 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 265 through 275 Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.738A pdb=" N ALA H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 181 Processing helix chain 'H' and resid 186 through 189 No H-bonds generated for 'chain 'H' and resid 186 through 189' Processing helix chain 'H' and resid 202 through 214 Processing helix chain 'H' and resid 227 through 237 Processing helix chain 'H' and resid 241 through 258 Processing helix chain 'H' and resid 265 through 273 Processing helix chain 'I' and resid 18 through 29 Processing helix chain 'I' and resid 37 through 52 removed outlier: 3.540A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 151 through 164 removed outlier: 3.999A pdb=" N ALA I 155 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP I 156 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 3.755A pdb=" N ALA I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 189 Processing helix chain 'I' and resid 202 through 213 Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 241 through 258 Processing helix chain 'I' and resid 265 through 273 Processing helix chain 'J' and resid 18 through 29 Processing helix chain 'J' and resid 37 through 52 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 102 through 112 Processing helix chain 'J' and resid 122 through 136 Processing helix chain 'J' and resid 151 through 164 removed outlier: 3.865A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 3.654A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 189 Processing helix chain 'J' and resid 202 through 214 Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 273 Processing helix chain 'K' and resid 18 through 29 Processing helix chain 'K' and resid 37 through 52 removed outlier: 3.749A pdb=" N ALA K 52 " --> pdb=" O GLY K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 76 Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 136 Processing helix chain 'K' and resid 151 through 163 removed outlier: 4.204A pdb=" N ALA K 155 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP K 163 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 181 Processing helix chain 'K' and resid 185 through 189 Processing helix chain 'K' and resid 202 through 213 Processing helix chain 'K' and resid 227 through 237 Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 265 through 275 Processing helix chain 'Q' and resid 22 through 33 Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 47 through 55 removed outlier: 3.663A pdb=" N VAL Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU Q 54 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 74 removed outlier: 3.827A pdb=" N ILE Q 70 " --> pdb=" O GLU Q 66 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 84 removed outlier: 3.872A pdb=" N MET Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 106 Processing helix chain 'Q' and resid 112 through 115 Processing helix chain 'Q' and resid 143 through 145 No H-bonds generated for 'chain 'Q' and resid 143 through 145' Processing helix chain 'Q' and resid 160 through 163 Processing helix chain 'X' and resid 5 through 14 Processing helix chain 'X' and resid 25 through 45 removed outlier: 4.275A pdb=" N GLY X 41 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS X 42 " --> pdb=" O HIS X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 73 removed outlier: 4.112A pdb=" N GLY X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 85 Processing sheet with id= A, first strand: chain 'A' and resid 314 through 316 removed outlier: 4.667A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 447 through 452 removed outlier: 6.042A pdb=" N ASP A 465 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 471 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 542 through 546 removed outlier: 6.320A pdb=" N VAL A 607 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 545 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU A 609 " --> pdb=" O LEU A 545 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.905A pdb=" N MET E 140 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE E 94 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE E 142 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA E 167 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE E 143 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL E 169 " --> pdb=" O ILE E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.540A pdb=" N GLY F 172 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.868A pdb=" N MET G 140 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE G 94 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE G 142 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA G 167 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE G 143 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 169 " --> pdb=" O ILE G 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'H' and resid 193 through 195 removed outlier: 7.589A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU H 170 " --> pdb=" O CYS H 56 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY H 172 " --> pdb=" O VAL H 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.872A pdb=" N GLY I 172 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 92 " --> pdb=" O MET I 140 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 56 through 59 removed outlier: 6.240A pdb=" N ALA J 192 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL J 59 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU J 194 " --> pdb=" O VAL J 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'J' and resid 91 through 94 removed outlier: 7.137A pdb=" N MET J 140 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE J 94 " --> pdb=" O MET J 140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE J 142 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA J 167 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE J 143 " --> pdb=" O ALA J 167 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL J 169 " --> pdb=" O ILE J 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.087A pdb=" N MET K 140 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE K 94 " --> pdb=" O MET K 140 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE K 142 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA K 167 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE K 143 " --> pdb=" O ALA K 167 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL K 169 " --> pdb=" O ILE K 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 988 hydrogen bonds defined for protein. 2874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 11.73 Time building geometry restraints manager: 14.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5624 1.33 - 1.45: 8100 1.45 - 1.57: 15030 1.57 - 1.69: 684 1.69 - 1.81: 126 Bond restraints: 29564 Sorted by residual: bond pdb=" N PRO I 79 " pdb=" CD PRO I 79 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" N ASN Q 59 " pdb=" CA ASN Q 59 " ideal model delta sigma weight residual 1.462 1.489 -0.028 9.50e-03 1.11e+04 8.58e+00 bond pdb=" N LYS F 66 " pdb=" CA LYS F 66 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.47e+00 bond pdb=" N VAL I 68 " pdb=" CA VAL I 68 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.52e+00 bond pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.43e+00 ... (remaining 29559 not shown) Histogram of bond angle deviations from ideal: 98.42 - 106.71: 2460 106.71 - 115.00: 18503 115.00 - 123.29: 18198 123.29 - 131.58: 2159 131.58 - 139.88: 141 Bond angle restraints: 41461 Sorted by residual: angle pdb=" N ASN Q 59 " pdb=" CA ASN Q 59 " pdb=" C ASN Q 59 " ideal model delta sigma weight residual 113.25 107.53 5.72 1.30e+00 5.92e-01 1.94e+01 angle pdb=" N ASP H 147 " pdb=" CA ASP H 147 " pdb=" C ASP H 147 " ideal model delta sigma weight residual 112.72 107.83 4.89 1.14e+00 7.69e-01 1.84e+01 angle pdb=" N ASP F 147 " pdb=" CA ASP F 147 " pdb=" C ASP F 147 " ideal model delta sigma weight residual 113.02 108.03 4.99 1.20e+00 6.94e-01 1.73e+01 angle pdb=" CA GLN F 213 " pdb=" CB GLN F 213 " pdb=" CG GLN F 213 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" N PRO Q 60 " pdb=" CA PRO Q 60 " pdb=" C PRO Q 60 " ideal model delta sigma weight residual 112.47 104.62 7.85 2.06e+00 2.36e-01 1.45e+01 ... (remaining 41456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 16024 35.96 - 71.93: 1041 71.93 - 107.89: 60 107.89 - 143.86: 6 143.86 - 179.82: 12 Dihedral angle restraints: 17143 sinusoidal: 9384 harmonic: 7759 Sorted by residual: dihedral pdb=" O4' U B 23 " pdb=" C1' U B 23 " pdb=" N1 U B 23 " pdb=" C2 U B 23 " ideal model delta sinusoidal sigma weight residual -128.00 51.03 -179.03 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 129 " pdb=" C1' U B 129 " pdb=" N1 U B 129 " pdb=" C2 U B 129 " ideal model delta sinusoidal sigma weight residual 232.00 54.85 177.15 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 138 " pdb=" C1' U B 138 " pdb=" N1 U B 138 " pdb=" C2 U B 138 " ideal model delta sinusoidal sigma weight residual 232.00 54.94 177.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 17140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3742 0.042 - 0.085: 818 0.085 - 0.127: 251 0.127 - 0.169: 23 0.169 - 0.211: 6 Chirality restraints: 4840 Sorted by residual: chirality pdb=" C3' G B 15 " pdb=" C4' G B 15 " pdb=" O3' G B 15 " pdb=" C2' G B 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" P G B 15 " pdb=" OP1 G B 15 " pdb=" OP2 G B 15 " pdb=" O5' G B 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.61 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CB ILE I 142 " pdb=" CA ILE I 142 " pdb=" CG1 ILE I 142 " pdb=" CG2 ILE I 142 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 4837 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 89 " -0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO H 90 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO H 90 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 90 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 59 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C ASN Q 59 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN Q 59 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO Q 60 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 213 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" CD GLN F 213 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN F 213 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN F 213 " 0.014 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 297 2.57 - 3.15: 23076 3.15 - 3.73: 52229 3.73 - 4.32: 67994 4.32 - 4.90: 102759 Nonbonded interactions: 246355 Sorted by model distance: nonbonded pdb=" O1B ATP J 301 " pdb="MG MG J 302 " model vdw 1.983 2.170 nonbonded pdb=" O1B ATP K 301 " pdb="MG MG K 302 " model vdw 1.986 2.170 nonbonded pdb=" OG1 THR J 67 " pdb="MG MG J 302 " model vdw 2.040 2.170 nonbonded pdb=" O1G ATP K 301 " pdb="MG MG K 302 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP G 301 " pdb="MG MG G 302 " model vdw 2.082 2.170 ... (remaining 246350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 276 \ or resid 301 through 302)) selection = (chain 'F' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'G' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 276 \ or resid 301 through 302)) selection = (chain 'H' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 276 \ or resid 301 through 302)) selection = (chain 'I' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 276 \ or resid 301 through 302)) selection = (chain 'J' and (resid 17 through 260 or (resid 261 through 264 and (name N or na \ me CA or name C or name O or name CB )) or resid 265 through 276 or resid 301 th \ rough 302)) selection = (chain 'K' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 276 \ or resid 301 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 346 5.49 5 Mg 7 5.21 5 S 85 5.16 5 C 16621 2.51 5 N 5150 2.21 5 O 6187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 27.130 Check model and map are aligned: 0.430 Process input model: 86.720 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 29564 Z= 0.239 Angle : 0.623 9.062 41461 Z= 0.354 Chirality : 0.040 0.211 4840 Planarity : 0.004 0.096 4076 Dihedral : 20.376 179.825 12115 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2649 helix: 0.96 (0.13), residues: 1524 sheet: -1.61 (0.43), residues: 141 loop : -1.09 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 114 average time/residue: 0.4473 time to fit residues: 81.7267 Evaluate side-chains 104 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3532 time to fit residues: 6.8827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 173 optimal weight: 40.0000 chunk 270 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 98 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 29564 Z= 0.300 Angle : 0.591 7.905 41461 Z= 0.315 Chirality : 0.040 0.187 4840 Planarity : 0.005 0.072 4076 Dihedral : 18.915 179.882 6747 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2649 helix: 1.01 (0.13), residues: 1527 sheet: -1.70 (0.43), residues: 143 loop : -1.10 (0.19), residues: 979 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 102 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 36 residues processed: 167 average time/residue: 0.3845 time to fit residues: 105.2432 Evaluate side-chains 136 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2771 time to fit residues: 22.5043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 271 optimal weight: 50.0000 chunk 292 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 29564 Z= 0.255 Angle : 0.561 7.926 41461 Z= 0.300 Chirality : 0.039 0.185 4840 Planarity : 0.004 0.062 4076 Dihedral : 18.841 179.694 6747 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2649 helix: 1.07 (0.13), residues: 1529 sheet: -1.07 (0.35), residues: 230 loop : -1.17 (0.20), residues: 890 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 110 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 23 residues processed: 166 average time/residue: 0.4267 time to fit residues: 114.0121 Evaluate side-chains 123 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3097 time to fit residues: 15.8759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 272 optimal weight: 0.3980 chunk 288 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 29564 Z= 0.228 Angle : 0.545 9.351 41461 Z= 0.291 Chirality : 0.038 0.184 4840 Planarity : 0.004 0.057 4076 Dihedral : 18.772 179.452 6747 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2649 helix: 1.16 (0.14), residues: 1528 sheet: -0.97 (0.35), residues: 228 loop : -1.10 (0.20), residues: 893 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 106 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 32 residues processed: 161 average time/residue: 0.4149 time to fit residues: 112.4657 Evaluate side-chains 133 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2689 time to fit residues: 19.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 4 optimal weight: 0.4980 chunk 214 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 245 optimal weight: 40.0000 chunk 199 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 258 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 29564 Z= 0.386 Angle : 0.635 13.016 41461 Z= 0.336 Chirality : 0.042 0.192 4840 Planarity : 0.005 0.060 4076 Dihedral : 18.810 178.023 6747 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2649 helix: 0.91 (0.13), residues: 1530 sheet: -1.05 (0.33), residues: 245 loop : -1.26 (0.20), residues: 874 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 104 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 32 residues processed: 161 average time/residue: 0.4308 time to fit residues: 113.7044 Evaluate side-chains 135 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 3.006 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2904 time to fit residues: 20.7943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 151 optimal weight: 0.3980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 29564 Z= 0.152 Angle : 0.522 13.138 41461 Z= 0.276 Chirality : 0.036 0.179 4840 Planarity : 0.004 0.050 4076 Dihedral : 18.681 178.241 6747 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2649 helix: 1.26 (0.14), residues: 1533 sheet: -0.95 (0.34), residues: 228 loop : -1.05 (0.20), residues: 888 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 9 residues processed: 146 average time/residue: 0.4337 time to fit residues: 103.0159 Evaluate side-chains 112 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 3.143 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3323 time to fit residues: 9.1999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 0.0050 chunk 210 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 242 optimal weight: 40.0000 chunk 161 optimal weight: 9.9990 chunk 287 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 175 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 29564 Z= 0.141 Angle : 0.511 12.794 41461 Z= 0.271 Chirality : 0.036 0.173 4840 Planarity : 0.004 0.051 4076 Dihedral : 18.510 179.347 6747 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2649 helix: 1.37 (0.14), residues: 1538 sheet: -0.79 (0.33), residues: 243 loop : -0.97 (0.21), residues: 868 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 133 average time/residue: 0.4308 time to fit residues: 93.4554 Evaluate side-chains 111 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 2.946 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2585 time to fit residues: 5.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 29564 Z= 0.216 Angle : 0.542 12.425 41461 Z= 0.286 Chirality : 0.037 0.176 4840 Planarity : 0.004 0.053 4076 Dihedral : 18.481 179.975 6747 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2649 helix: 1.31 (0.14), residues: 1536 sheet: -0.77 (0.33), residues: 243 loop : -1.00 (0.21), residues: 870 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 119 average time/residue: 0.4316 time to fit residues: 85.4648 Evaluate side-chains 113 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3390 time to fit residues: 7.3241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 267 optimal weight: 50.0000 chunk 161 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 241 optimal weight: 30.0000 chunk 253 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 29564 Z= 0.242 Angle : 0.558 12.065 41461 Z= 0.295 Chirality : 0.038 0.176 4840 Planarity : 0.004 0.054 4076 Dihedral : 18.508 179.754 6747 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2649 helix: 1.22 (0.14), residues: 1535 sheet: -0.82 (0.33), residues: 243 loop : -0.98 (0.21), residues: 871 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.4218 time to fit residues: 83.4865 Evaluate side-chains 113 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 2.994 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2988 time to fit residues: 9.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 30.0000 chunk 283 optimal weight: 3.9990 chunk 172 optimal weight: 30.0000 chunk 134 optimal weight: 0.6980 chunk 196 optimal weight: 40.0000 chunk 296 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 29564 Z= 0.204 Angle : 0.542 12.129 41461 Z= 0.287 Chirality : 0.037 0.172 4840 Planarity : 0.004 0.060 4076 Dihedral : 18.481 179.883 6747 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2649 helix: 1.21 (0.14), residues: 1522 sheet: -0.82 (0.33), residues: 243 loop : -0.92 (0.21), residues: 884 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.4428 time to fit residues: 79.1357 Evaluate side-chains 106 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2651 time to fit residues: 4.5878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 40.0000 chunk 251 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.080964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.057220 restraints weight = 134364.205| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.62 r_work: 0.3201 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 29564 Z= 0.331 Angle : 0.611 11.687 41461 Z= 0.323 Chirality : 0.041 0.177 4840 Planarity : 0.004 0.059 4076 Dihedral : 18.558 178.824 6747 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2649 helix: 0.99 (0.13), residues: 1530 sheet: -1.02 (0.32), residues: 247 loop : -0.98 (0.21), residues: 872 =============================================================================== Job complete usr+sys time: 5122.44 seconds wall clock time: 95 minutes 31.92 seconds (5731.92 seconds total)